It is quite easy to get in a situation like you describe if you have a volume exported manually and in a host set. This effectively leaves the same targets presented more than once with different LUN ID's. As long as you have multipathing setup you should be able to remove duplicate LUNs without down time. You can see which VLUNs a host has with showvlun, and remove them with removevlun.

I would suggest testing it on a test host first but in principle I can see no issue with removing the duplicate.